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- PDB-8zxd: the Planar Cell Polarity Core Protein Vangl1 -

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Basic information

Entry
Database: PDB / ID: 8zxd
Titlethe Planar Cell Polarity Core Protein Vangl1
ComponentsVang-like protein 1
KeywordsSTRUCTURAL PROTEIN / NTD / PCP / Vangl / Prickle
Function / homology
Function and homology information


mucociliary clearance / RHOD GTPase cycle / RHOF GTPase cycle / RND1 GTPase cycle / Wnt signaling pathway, planar cell polarity pathway / RND2 GTPase cycle / RND3 GTPase cycle / RHOB GTPase cycle / RHOV GTPase cycle / pigmentation ...mucociliary clearance / RHOD GTPase cycle / RHOF GTPase cycle / RND1 GTPase cycle / Wnt signaling pathway, planar cell polarity pathway / RND2 GTPase cycle / RND3 GTPase cycle / RHOB GTPase cycle / RHOV GTPase cycle / pigmentation / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / lateral plasma membrane / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / extracellular region / plasma membrane
Similarity search - Function
Vang-like protein / Strabismus protein
Similarity search - Domain/homology
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / CHOLESTEROL HEMISUCCINATE / Vang-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang, F. / Chen, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82101213 China
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structure and oligomerization of the human planar cell polarity core protein Vangl1.
Authors: Fan Zhang / Shaobai Li / Hao Wu / Shanshuang Chen /
Abstract: Vangl is a planar cell polarity (PCP) core protein essential for aligned cell orientation along the epithelial plane perpendicular to the apical-basal direction, which is important for tissue ...Vangl is a planar cell polarity (PCP) core protein essential for aligned cell orientation along the epithelial plane perpendicular to the apical-basal direction, which is important for tissue morphogenesis, development and collective cell behavior. Mutations in Vangl are associated with developmental defects, including neural tube defects (NTDs), according to human cohort studies of sporadic and familial cases. The complex mechanisms underlying Vangl-mediated PCP signaling or Vangl-associated human congenital diseases have been hampered by the lack of molecular characterizations of Vangl. Here, we show biochemical and structural evidence that human Vangl1 oligomerizes as dimers of trimers, and that the dimerization of trimers promotes binding to the PCP effector Prickle1 (Pk1) in vitro. Mapping of human disease-associated point mutations suggests potential pathological mechanisms and paves the way for future studies on the importance of lipid binding, central vestibule and oligomerization of Vangl, thereby providing insights into the molecular mechanisms of the PCP signaling pathway.
History
DepositionJun 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
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Revision 1.1Mar 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vang-like protein 1
B: Vang-like protein 1
C: Vang-like protein 1
D: Vang-like protein 1
E: Vang-like protein 1
F: Vang-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,23224
Polymers360,3236
Non-polymers9,90818
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Vang-like protein 1 / Loop-tail protein 2 homolog / LPP2 / Strabismus 2 / Van Gogh-like protein 1


Mass: 60053.887 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VANGL1, STB2 / Production host: Homo sapiens (human) / References: UniProt: Q8TAA9
#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C36H72NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vang-like protein 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 718127 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00119962
ELECTRON MICROSCOPYf_angle_d0.39827048
ELECTRON MICROSCOPYf_dihedral_angle_d4.5332820
ELECTRON MICROSCOPYf_chiral_restr0.0343078
ELECTRON MICROSCOPYf_plane_restr0.0033318

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